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<a href="container__prd_8hh.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">// Voro++, a 3D cell-based Voronoi library</span>
<a name="l00002"></a>00002 <span class="comment">//</span>
<a name="l00003"></a>00003 <span class="comment">// Author   : Chris H. Rycroft (LBL / UC Berkeley)</span>
<a name="l00004"></a>00004 <span class="comment">// Email    : chr@alum.mit.edu</span>
<a name="l00005"></a>00005 <span class="comment">// Date     : August 30th 2011</span>
<a name="l00006"></a>00006 <span class="comment"></span>
<a name="l00007"></a>00007 <span class="comment">/** \file container_prd.hh</span>
<a name="l00008"></a>00008 <span class="comment"> * \brief Header file for the container_periodic_base and related classes. */</span>
<a name="l00009"></a>00009 
<a name="l00010"></a>00010 <span class="preprocessor">#ifndef VOROPP_CONTAINER_PRD_HH</span>
<a name="l00011"></a>00011 <span class="preprocessor"></span><span class="preprocessor">#define VOROPP_CONTAINER_PRD_HH</span>
<a name="l00012"></a>00012 <span class="preprocessor"></span>
<a name="l00013"></a>00013 <span class="preprocessor">#include &lt;cstdio&gt;</span>
<a name="l00014"></a>00014 <span class="preprocessor">#include &lt;cstdlib&gt;</span>
<a name="l00015"></a>00015 <span class="preprocessor">#include &lt;cmath&gt;</span>
<a name="l00016"></a>00016 <span class="preprocessor">#include &lt;vector&gt;</span>
<a name="l00017"></a>00017 <span class="keyword">using namespace </span>std;
<a name="l00018"></a>00018 
<a name="l00019"></a>00019 <span class="preprocessor">#include &quot;<a class="code" href="config_8hh.html" title="Master configuration file for setting various compile-time options.">config.hh</a>&quot;</span>
<a name="l00020"></a>00020 <span class="preprocessor">#include &quot;<a class="code" href="common_8hh.html" title="Header file for the small helper functions.">common.hh</a>&quot;</span>
<a name="l00021"></a>00021 <span class="preprocessor">#include &quot;<a class="code" href="v__base_8hh.html" title="Header file for the base Voronoi container class.">v_base.hh</a>&quot;</span>
<a name="l00022"></a>00022 <span class="preprocessor">#include &quot;<a class="code" href="cell_8hh.html" title="Header file for the voronoicell and related classes.">cell.hh</a>&quot;</span>
<a name="l00023"></a>00023 <span class="preprocessor">#include &quot;<a class="code" href="c__loops_8hh.html" title="Header file for the loop classes.">c_loops.hh</a>&quot;</span>
<a name="l00024"></a>00024 <span class="preprocessor">#include &quot;<a class="code" href="v__compute_8hh.html" title="Header file for the voro_compute template and related classes.">v_compute.hh</a>&quot;</span>
<a name="l00025"></a>00025 <span class="preprocessor">#include &quot;<a class="code" href="unitcell_8hh.html" title="Header file for the unitcell class.">unitcell.hh</a>&quot;</span>
<a name="l00026"></a>00026 <span class="preprocessor">#include &quot;<a class="code" href="rad__option_8hh.html" title="Header file for the classes encapsulating functionality for the regular and radical Voronoi tessellat...">rad_option.hh</a>&quot;</span>
<a name="l00027"></a>00027 
<a name="l00028"></a>00028 <span class="keyword">namespace </span>voro {
<a name="l00029"></a>00029 <span class="comment"></span>
<a name="l00030"></a>00030 <span class="comment">/** \brief Class for representing a particle system in a 3D periodic</span>
<a name="l00031"></a>00031 <span class="comment"> * non-orthogonal periodic domain.</span>
<a name="l00032"></a>00032 <span class="comment"> *</span>
<a name="l00033"></a>00033 <span class="comment"> * This class represents a particle system in a three-dimensional</span>
<a name="l00034"></a>00034 <span class="comment"> * non-orthogonal periodic domain. The domain is defined by three periodicity</span>
<a name="l00035"></a>00035 <span class="comment"> * vectors (bx,0,0), (bxy,by,0), and (bxz,byz,bz) that represent a</span>
<a name="l00036"></a>00036 <span class="comment"> * parallelepiped. Internally, the class stores particles in the box 0&lt;x&lt;bx,</span>
<a name="l00037"></a>00037 <span class="comment"> * 0&lt;y&lt;by, 0&lt;z&lt;bz, and constructs periodic images of particles that displaced</span>
<a name="l00038"></a>00038 <span class="comment"> * by the three periodicity vectors when they are necessary for the</span>
<a name="l00039"></a>00039 <span class="comment"> * computation. The internal memory structure for this class is significantly</span>
<a name="l00040"></a>00040 <span class="comment"> * different from the container_base class in order to handle the dynamic</span>
<a name="l00041"></a>00041 <span class="comment"> * construction of these periodic images.</span>
<a name="l00042"></a>00042 <span class="comment"> *</span>
<a name="l00043"></a>00043 <span class="comment"> * The class is derived from the unitcell class, which encapsulates information</span>
<a name="l00044"></a>00044 <span class="comment"> * about the domain geometry, and the voro_base class, which encapsulates</span>
<a name="l00045"></a>00045 <span class="comment"> * information about the underlying computational grid. */</span>
<a name="l00046"></a><a class="code" href="classvoro_1_1container__periodic__base.html">00046</a> <span class="keyword">class </span><a class="code" href="classvoro_1_1container__periodic__base.html" title="Class for representing a particle system in a 3D periodic non-orthogonal periodic domain...">container_periodic_base</a> : <span class="keyword">public</span> <a class="code" href="classvoro_1_1unitcell.html" title="Class for computation of the unit Voronoi cell associated with a 3D non-rectangular periodic domain...">unitcell</a>, <span class="keyword">public</span> <a class="code" href="classvoro_1_1voro__base.html" title="Class containing data structures common across all particle container classes.">voro_base</a> {
<a name="l00047"></a>00047         <span class="keyword">public</span>:<span class="comment"></span>
<a name="l00048"></a>00048 <span class="comment">                /** The lower y index (inclusive) of the primary domain within</span>
<a name="l00049"></a>00049 <span class="comment">                 * the block structure. */</span>
<a name="l00050"></a><a class="code" href="classvoro_1_1container__periodic__base.html#a407b759a2c2d6baec5183e18a726a4e6">00050</a>                 <span class="keywordtype">int</span> <a class="code" href="classvoro_1_1container__periodic__base.html#a407b759a2c2d6baec5183e18a726a4e6">ey</a>;<span class="comment"></span>
<a name="l00051"></a>00051 <span class="comment">                /** The lower z index (inclusive) of the primary domain within</span>
<a name="l00052"></a>00052 <span class="comment">                 * the block structure. */</span>
<a name="l00053"></a><a class="code" href="classvoro_1_1container__periodic__base.html#a9920ab99f51190399ceda8fb8689364f">00053</a>                 <span class="keywordtype">int</span> <a class="code" href="classvoro_1_1container__periodic__base.html#a9920ab99f51190399ceda8fb8689364f">ez</a>;<span class="comment"></span>
<a name="l00054"></a>00054 <span class="comment">                /** The upper y index (exclusive) of the primary domain within</span>
<a name="l00055"></a>00055 <span class="comment">                 * the block structure. */</span>
<a name="l00056"></a><a class="code" href="classvoro_1_1container__periodic__base.html#a012ffc20dd6379bcbd26ddc0c5cc8591">00056</a>                 <span class="keywordtype">int</span> <a class="code" href="classvoro_1_1container__periodic__base.html#a012ffc20dd6379bcbd26ddc0c5cc8591">wy</a>;<span class="comment"></span>
<a name="l00057"></a>00057 <span class="comment">                /** The upper z index (exclusive) of the primary domain within</span>
<a name="l00058"></a>00058 <span class="comment">                 * the block structure. */</span>
<a name="l00059"></a><a class="code" href="classvoro_1_1container__periodic__base.html#afe16d21568925f78421122cdfb7b0cc0">00059</a>                 <span class="keywordtype">int</span> <a class="code" href="classvoro_1_1container__periodic__base.html#afe16d21568925f78421122cdfb7b0cc0">wz</a>;<span class="comment"></span>
<a name="l00060"></a>00060 <span class="comment">                /** The total size of the block structure (including images) in</span>
<a name="l00061"></a>00061 <span class="comment">                 * the y direction. */</span>
<a name="l00062"></a><a class="code" href="classvoro_1_1container__periodic__base.html#aa143ce1ecd9093f7c1889a0481b4cbb5">00062</a>                 <span class="keywordtype">int</span> <a class="code" href="classvoro_1_1container__periodic__base.html#aa143ce1ecd9093f7c1889a0481b4cbb5">oy</a>;<span class="comment"></span>
<a name="l00063"></a>00063 <span class="comment">                /** The total size of the block structure (including images) in</span>
<a name="l00064"></a>00064 <span class="comment">                 * the z direction. */</span>
<a name="l00065"></a><a class="code" href="classvoro_1_1container__periodic__base.html#ab1f18c51495f684dfc4d3372f9b311da">00065</a>                 <span class="keywordtype">int</span> <a class="code" href="classvoro_1_1container__periodic__base.html#ab1f18c51495f684dfc4d3372f9b311da">oz</a>;<span class="comment"></span>
<a name="l00066"></a>00066 <span class="comment">                /** The total number of blocks. */</span>
<a name="l00067"></a><a class="code" href="classvoro_1_1container__periodic__base.html#ae1dfc876e56ec254053c7672b4454313">00067</a>                 <span class="keywordtype">int</span> <a class="code" href="classvoro_1_1container__periodic__base.html#ae1dfc876e56ec254053c7672b4454313">oxyz</a>;<span class="comment"></span>
<a name="l00068"></a>00068 <span class="comment">                /** This array holds the numerical IDs of each particle in each</span>
<a name="l00069"></a>00069 <span class="comment">                 * computational box. */</span>
<a name="l00070"></a><a class="code" href="classvoro_1_1container__periodic__base.html#a5abecf243780e08dd6cce6f5dd270c76">00070</a>                 <span class="keywordtype">int</span> **<a class="code" href="classvoro_1_1container__periodic__base.html#a5abecf243780e08dd6cce6f5dd270c76">id</a>;<span class="comment"></span>
<a name="l00071"></a>00071 <span class="comment">                /** A two dimensional array holding particle positions. For the</span>
<a name="l00072"></a>00072 <span class="comment">                 * derived container_poly class, this also holds particle</span>
<a name="l00073"></a>00073 <span class="comment">                 * radii. */</span>
<a name="l00074"></a><a class="code" href="classvoro_1_1container__periodic__base.html#a301925d00d1d79f3df7b965d02e25608">00074</a>                 <span class="keywordtype">double</span> **<a class="code" href="classvoro_1_1container__periodic__base.html#a301925d00d1d79f3df7b965d02e25608">p</a>;<span class="comment"></span>
<a name="l00075"></a>00075 <span class="comment">                /** This array holds the number of particles within each</span>
<a name="l00076"></a>00076 <span class="comment">                 * computational box of the container. */</span>
<a name="l00077"></a><a class="code" href="classvoro_1_1container__periodic__base.html#a8ae965b9dbb02a92e8dcb0d082d625a2">00077</a>                 <span class="keywordtype">int</span> *<a class="code" href="classvoro_1_1container__periodic__base.html#a8ae965b9dbb02a92e8dcb0d082d625a2">co</a>;<span class="comment"></span>
<a name="l00078"></a>00078 <span class="comment">                /** This array holds the maximum amount of particle memory for</span>
<a name="l00079"></a>00079 <span class="comment">                 * each computational box of the container. If the number of</span>
<a name="l00080"></a>00080 <span class="comment">                 * particles in a particular box ever approaches this limit,</span>
<a name="l00081"></a>00081 <span class="comment">                 * more is allocated using the add_particle_memory() function.</span>
<a name="l00082"></a>00082 <span class="comment">                 */</span>
<a name="l00083"></a><a class="code" href="classvoro_1_1container__periodic__base.html#a4ff4effc81e7b8908cda31f0c8c5ad70">00083</a>                 <span class="keywordtype">int</span> *<a class="code" href="classvoro_1_1container__periodic__base.html#a4ff4effc81e7b8908cda31f0c8c5ad70">mem</a>;<span class="comment"></span>
<a name="l00084"></a>00084 <span class="comment">                /** An array holding information about periodic image</span>
<a name="l00085"></a>00085 <span class="comment">                 * construction at a given location. */</span>
<a name="l00086"></a><a class="code" href="classvoro_1_1container__periodic__base.html#a90658551a7621bedfea141f052443fe1">00086</a>                 <span class="keywordtype">char</span> *<a class="code" href="classvoro_1_1container__periodic__base.html#a90658551a7621bedfea141f052443fe1">img</a>;<span class="comment"></span>
<a name="l00087"></a>00087 <span class="comment">                /** The initial amount of memory to allocate for particles</span>
<a name="l00088"></a>00088 <span class="comment">                 * for each block. */</span>
<a name="l00089"></a><a class="code" href="classvoro_1_1container__periodic__base.html#adeaa9eab58ba59f2fa3d7176ce617ff1">00089</a>                 <span class="keyword">const</span> <span class="keywordtype">int</span> <a class="code" href="classvoro_1_1container__periodic__base.html#adeaa9eab58ba59f2fa3d7176ce617ff1">init_mem</a>;<span class="comment"></span>
<a name="l00090"></a>00090 <span class="comment">                /** The amount of memory in the array structure for each</span>
<a name="l00091"></a>00091 <span class="comment">                 * particle. This is set to 3 when the basic class is</span>
<a name="l00092"></a>00092 <span class="comment">                 * initialized, so that the array holds (x,y,z) positions. If</span>
<a name="l00093"></a>00093 <span class="comment">                 * the container class is initialized as part of the derived</span>
<a name="l00094"></a>00094 <span class="comment">                 * class container_poly, then this is set to 4, to also hold</span>
<a name="l00095"></a>00095 <span class="comment">                 * the particle radii. */</span>
<a name="l00096"></a><a class="code" href="classvoro_1_1container__periodic__base.html#a5213538964cf869c9751a27bccaf323e">00096</a>                 <span class="keyword">const</span> <span class="keywordtype">int</span> <a class="code" href="classvoro_1_1container__periodic__base.html#a5213538964cf869c9751a27bccaf323e">ps</a>;
<a name="l00097"></a>00097                 <a class="code" href="classvoro_1_1container__periodic__base.html" title="Class for representing a particle system in a 3D periodic non-orthogonal periodic domain...">container_periodic_base</a>(<span class="keywordtype">double</span> bx_,<span class="keywordtype">double</span> bxy_,<span class="keywordtype">double</span> by_,<span class="keywordtype">double</span> bxz_,<span class="keywordtype">double</span> byz_,<span class="keywordtype">double</span> bz_,
<a name="l00098"></a>00098                                 <span class="keywordtype">int</span> nx_,<span class="keywordtype">int</span> ny_,<span class="keywordtype">int</span> nz_,<span class="keywordtype">int</span> init_mem_,<span class="keywordtype">int</span> ps);
<a name="l00099"></a>00099                 ~<a class="code" href="classvoro_1_1container__periodic__base.html" title="Class for representing a particle system in a 3D periodic non-orthogonal periodic domain...">container_periodic_base</a>();<span class="comment"></span>
<a name="l00100"></a>00100 <span class="comment">                /** Prints all particles in the container, including those that</span>
<a name="l00101"></a>00101 <span class="comment">                 * have been constructed in image blocks. */</span>
<a name="l00102"></a><a class="code" href="classvoro_1_1container__periodic__base.html#ac931a6c1cab4b2e910a0d07969b38785">00102</a>                 <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic__base.html#ac931a6c1cab4b2e910a0d07969b38785">print_all_particles</a>() {
<a name="l00103"></a>00103                         <span class="keywordtype">int</span> ijk,q;
<a name="l00104"></a>00104                         <span class="keywordflow">for</span>(ijk=0;ijk&lt;oxyz;ijk++) <span class="keywordflow">for</span>(q=0;q&lt;co[ijk];q++)
<a name="l00105"></a>00105                                 printf(<span class="stringliteral">&quot;%d %g %g %g\n&quot;</span>,<span class="keywordtype">id</span>[ijk][q],p[ijk][ps*q],p[ijk][ps*q+1],p[ijk][ps*q+2]);
<a name="l00106"></a>00106                 }
<a name="l00107"></a>00107                 <span class="keywordtype">void</span> region_count();<span class="comment"></span>
<a name="l00108"></a>00108 <span class="comment">                /** Initializes the Voronoi cell prior to a compute_cell</span>
<a name="l00109"></a>00109 <span class="comment">                 * operation for a specific particle being carried out by a</span>
<a name="l00110"></a>00110 <span class="comment">                 * voro_compute class. The cell is initialized to be the</span>
<a name="l00111"></a>00111 <span class="comment">                 * pre-computed unit Voronoi cell based on planes formed by</span>
<a name="l00112"></a>00112 <span class="comment">                 * periodic images of the particle.</span>
<a name="l00113"></a>00113 <span class="comment">                 * \param[in,out] c a reference to a voronoicell object.</span>
<a name="l00114"></a>00114 <span class="comment">                 * \param[in] ijk the block that the particle is within.</span>
<a name="l00115"></a>00115 <span class="comment">                 * \param[in] q the index of the particle within its block.</span>
<a name="l00116"></a>00116 <span class="comment">                 * \param[in] (ci,cj,ck) the coordinates of the block in the</span>
<a name="l00117"></a>00117 <span class="comment">                 *                       container coordinate system.</span>
<a name="l00118"></a>00118 <span class="comment">                 * \param[out] (i,j,k) the coordinates of the test block</span>
<a name="l00119"></a>00119 <span class="comment">                 *                     relative to the voro_compute</span>
<a name="l00120"></a>00120 <span class="comment">                 *                     coordinate system.</span>
<a name="l00121"></a>00121 <span class="comment">                 * \param[out] (x,y,z) the position of the particle.</span>
<a name="l00122"></a>00122 <span class="comment">                 * \param[out] disp a block displacement used internally by the</span>
<a name="l00123"></a>00123 <span class="comment">                 *                  compute_cell routine.</span>
<a name="l00124"></a>00124 <span class="comment">                 * \return False if the plane cuts applied by walls completely</span>
<a name="l00125"></a>00125 <span class="comment">                 * removed the cell, true otherwise. */</span>
<a name="l00126"></a>00126                 <span class="keyword">template</span>&lt;<span class="keyword">class</span> v_cell&gt;
<a name="l00127"></a><a class="code" href="classvoro_1_1container__periodic__base.html#ae540389dc8845562c5f8cd45cec71edd">00127</a>                 <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="classvoro_1_1container__periodic__base.html#ae540389dc8845562c5f8cd45cec71edd">initialize_voronoicell</a>(v_cell &amp;c,<span class="keywordtype">int</span> ijk,<span class="keywordtype">int</span> q,<span class="keywordtype">int</span> ci,<span class="keywordtype">int</span> cj,<span class="keywordtype">int</span> ck,<span class="keywordtype">int</span> &amp;i,<span class="keywordtype">int</span> &amp;j,<span class="keywordtype">int</span> &amp;k,<span class="keywordtype">double</span> &amp;x,<span class="keywordtype">double</span> &amp;y,<span class="keywordtype">double</span> &amp;z,<span class="keywordtype">int</span> &amp;disp) {
<a name="l00128"></a>00128                         c=unit_voro;
<a name="l00129"></a>00129                         <span class="keywordtype">double</span> *pp=p[ijk]+ps*q;
<a name="l00130"></a>00130                         x=*(pp++);y=*(pp++);z=*pp;
<a name="l00131"></a>00131                         i=nx;j=ey;k=ez;
<a name="l00132"></a>00132                         <span class="keywordflow">return</span> <span class="keyword">true</span>;
<a name="l00133"></a>00133                 }<span class="comment"></span>
<a name="l00134"></a>00134 <span class="comment">                /** Initializes parameters for a find_voronoi_cell call within</span>
<a name="l00135"></a>00135 <span class="comment">                 * the voro_compute template.</span>
<a name="l00136"></a>00136 <span class="comment">                 * \param[in] (ci,cj,ck) the coordinates of the test block in</span>
<a name="l00137"></a>00137 <span class="comment">                 *                       the container coordinate system.</span>
<a name="l00138"></a>00138 <span class="comment">                 * \param[in] ijk the index of the test block</span>
<a name="l00139"></a>00139 <span class="comment">                 * \param[out] (i,j,k) the coordinates of the test block</span>
<a name="l00140"></a>00140 <span class="comment">                 *                     relative to the voro_compute</span>
<a name="l00141"></a>00141 <span class="comment">                 *                     coordinate system.</span>
<a name="l00142"></a>00142 <span class="comment">                 * \param[out] disp a block displacement used internally by the</span>
<a name="l00143"></a>00143 <span class="comment">                 *                  find_voronoi_cell routine (but not needed</span>
<a name="l00144"></a>00144 <span class="comment">                 *                  in this instance.) */</span>
<a name="l00145"></a><a class="code" href="classvoro_1_1container__periodic__base.html#a812ed5572fcfece48b73517fcf913ec0">00145</a>                 <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic__base.html#a812ed5572fcfece48b73517fcf913ec0">initialize_search</a>(<span class="keywordtype">int</span> ci,<span class="keywordtype">int</span> cj,<span class="keywordtype">int</span> ck,<span class="keywordtype">int</span> ijk,<span class="keywordtype">int</span> &amp;i,<span class="keywordtype">int</span> &amp;j,<span class="keywordtype">int</span> &amp;k,<span class="keywordtype">int</span> &amp;disp) {
<a name="l00146"></a>00146                         i=nx;j=ey;k=ez;
<a name="l00147"></a>00147                 }<span class="comment"></span>
<a name="l00148"></a>00148 <span class="comment">                /** Returns the position of a particle currently being computed</span>
<a name="l00149"></a>00149 <span class="comment">                 * relative to the computational block that it is within. It is</span>
<a name="l00150"></a>00150 <span class="comment">                 * used to select the optimal worklist entry to use.</span>
<a name="l00151"></a>00151 <span class="comment">                 * \param[in] (x,y,z) the position of the particle.</span>
<a name="l00152"></a>00152 <span class="comment">                 * \param[in] (ci,cj,ck) the block that the particle is within.</span>
<a name="l00153"></a>00153 <span class="comment">                 * \param[out] (fx,fy,fz) the position relative to the block.</span>
<a name="l00154"></a>00154 <span class="comment">                 */</span>
<a name="l00155"></a><a class="code" href="classvoro_1_1container__periodic__base.html#a4f637efc5e56874aa9d68f44505e042c">00155</a>                 <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic__base.html#a4f637efc5e56874aa9d68f44505e042c">frac_pos</a>(<span class="keywordtype">double</span> x,<span class="keywordtype">double</span> y,<span class="keywordtype">double</span> z,<span class="keywordtype">double</span> ci,<span class="keywordtype">double</span> cj,<span class="keywordtype">double</span> ck,<span class="keywordtype">double</span> &amp;fx,<span class="keywordtype">double</span> &amp;fy,<span class="keywordtype">double</span> &amp;fz) {
<a name="l00156"></a>00156                         fx=x-boxx*ci;
<a name="l00157"></a>00157                         fy=y-boxy*(cj-ey);
<a name="l00158"></a>00158                         fz=z-boxz*(ck-ez);
<a name="l00159"></a>00159                 }<span class="comment"></span>
<a name="l00160"></a>00160 <span class="comment">                /** Calculates the index of block in the container structure</span>
<a name="l00161"></a>00161 <span class="comment">                 * corresponding to given coordinates.</span>
<a name="l00162"></a>00162 <span class="comment">                 * \param[in] (ci,cj,ck) the coordinates of the original block</span>
<a name="l00163"></a>00163 <span class="comment">                 *                       in the current computation, relative</span>
<a name="l00164"></a>00164 <span class="comment">                 *                       to the container coordinate system.</span>
<a name="l00165"></a>00165 <span class="comment">                 * \param[in] (ei,ej,ek) the displacement of the current block</span>
<a name="l00166"></a>00166 <span class="comment">                 *                       from the original block.</span>
<a name="l00167"></a>00167 <span class="comment">                 * \param[in,out] (qx,qy,qz) the periodic displacement that</span>
<a name="l00168"></a>00168 <span class="comment">                 *                           must be added to the particles</span>
<a name="l00169"></a>00169 <span class="comment">                 *                           within the computed block.</span>
<a name="l00170"></a>00170 <span class="comment">                 * \param[in] disp a block displacement used internally by the</span>
<a name="l00171"></a>00171 <span class="comment">                 *                  find_voronoi_cell and compute_cell routines</span>
<a name="l00172"></a>00172 <span class="comment">                 *                  (but not needed in this instance.)</span>
<a name="l00173"></a>00173 <span class="comment">                 * \return The block index. */</span>
<a name="l00174"></a><a class="code" href="classvoro_1_1container__periodic__base.html#aa0cd2a5bf51968b7af3334f4bbb8df8e">00174</a>                 <span class="keyword">inline</span> <span class="keywordtype">int</span> <a class="code" href="classvoro_1_1container__periodic__base.html#aa0cd2a5bf51968b7af3334f4bbb8df8e">region_index</a>(<span class="keywordtype">int</span> ci,<span class="keywordtype">int</span> cj,<span class="keywordtype">int</span> ck,<span class="keywordtype">int</span> ei,<span class="keywordtype">int</span> ej,<span class="keywordtype">int</span> ek,<span class="keywordtype">double</span> &amp;qx,<span class="keywordtype">double</span> &amp;qy,<span class="keywordtype">double</span> &amp;qz,<span class="keywordtype">int</span> &amp;disp) {
<a name="l00175"></a>00175                         <span class="keywordtype">int</span> qi=ci+(ei-nx),qj=cj+(ej-ey),qk=ck+(ek-ez);
<a name="l00176"></a>00176                         <span class="keywordtype">int</span> iv(step_div(qi,nx));<span class="keywordflow">if</span>(iv!=0) {qx=iv*bx;qi-=nx*iv;} <span class="keywordflow">else</span> qx=0;
<a name="l00177"></a>00177                         create_periodic_image(qi,qj,qk);
<a name="l00178"></a>00178                         <span class="keywordflow">return</span> qi+nx*(qj+oy*qk);
<a name="l00179"></a>00179                 }
<a name="l00180"></a>00180                 <span class="keywordtype">void</span> create_all_images();
<a name="l00181"></a>00181                 <span class="keywordtype">void</span> check_compartmentalized();
<a name="l00182"></a>00182         <span class="keyword">protected</span>:
<a name="l00183"></a>00183                 <span class="keywordtype">void</span> add_particle_memory(<span class="keywordtype">int</span> i);
<a name="l00184"></a>00184                 <span class="keywordtype">void</span> put_locate_block(<span class="keywordtype">int</span> &amp;ijk,<span class="keywordtype">double</span> &amp;x,<span class="keywordtype">double</span> &amp;y,<span class="keywordtype">double</span> &amp;z);
<a name="l00185"></a>00185                 <span class="keywordtype">void</span> put_locate_block(<span class="keywordtype">int</span> &amp;ijk,<span class="keywordtype">double</span> &amp;x,<span class="keywordtype">double</span> &amp;y,<span class="keywordtype">double</span> &amp;z,<span class="keywordtype">int</span> &amp;ai,<span class="keywordtype">int</span> &amp;aj,<span class="keywordtype">int</span> &amp;ak);<span class="comment"></span>
<a name="l00186"></a>00186 <span class="comment">                /** Creates particles within an image block by copying them</span>
<a name="l00187"></a>00187 <span class="comment">                 * from the primary domain and shifting them. If the given</span>
<a name="l00188"></a>00188 <span class="comment">                 * block is aligned with the primary domain in the z-direction,</span>
<a name="l00189"></a>00189 <span class="comment">                 * the routine calls the simpler create_side_image routine</span>
<a name="l00190"></a>00190 <span class="comment">                 * where the image block may comprise of particles from up to</span>
<a name="l00191"></a>00191 <span class="comment">                 * two primary blocks. Otherwise is calls the more complex</span>
<a name="l00192"></a>00192 <span class="comment">                 * create_vertical_image where the image block may comprise of</span>
<a name="l00193"></a>00193 <span class="comment">                 * particles from up to four primary blocks.</span>
<a name="l00194"></a>00194 <span class="comment">                 * \param[in] (di,dj,dk) the coordinates of the image block to</span>
<a name="l00195"></a>00195 <span class="comment">                 *                       create. */</span>
<a name="l00196"></a><a class="code" href="classvoro_1_1container__periodic__base.html#a11b7428673e4791fe651036ecda0cd12">00196</a>                 <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic__base.html#a11b7428673e4791fe651036ecda0cd12">create_periodic_image</a>(<span class="keywordtype">int</span> di,<span class="keywordtype">int</span> dj,<span class="keywordtype">int</span> dk) {
<a name="l00197"></a>00197                         <span class="keywordflow">if</span>(di&lt;0||di&gt;=nx||dj&lt;0||dj&gt;=oy||dk&lt;0||dk&gt;=oz)
<a name="l00198"></a>00198                                 voro_fatal_error(<span class="stringliteral">&quot;Constructing periodic image for nonexistent point&quot;</span>,<a class="code" href="config_8hh.html#ad8e0de9d48da06e86dd87884e4a2d47e">VOROPP_INTERNAL_ERROR</a>);
<a name="l00199"></a>00199                         <span class="keywordflow">if</span>(dk&gt;=ez&amp;&amp;dk&lt;wz) {
<a name="l00200"></a>00200                                 <span class="keywordflow">if</span>(dj&lt;ey||dj&gt;=wy) create_side_image(di,dj,dk);
<a name="l00201"></a>00201                         } <span class="keywordflow">else</span> create_vertical_image(di,dj,dk);
<a name="l00202"></a>00202                 }
<a name="l00203"></a>00203                 <span class="keywordtype">void</span> create_side_image(<span class="keywordtype">int</span> di,<span class="keywordtype">int</span> dj,<span class="keywordtype">int</span> dk);
<a name="l00204"></a>00204                 <span class="keywordtype">void</span> create_vertical_image(<span class="keywordtype">int</span> di,<span class="keywordtype">int</span> dj,<span class="keywordtype">int</span> dk);
<a name="l00205"></a>00205                 <span class="keywordtype">void</span> put_image(<span class="keywordtype">int</span> reg,<span class="keywordtype">int</span> fijk,<span class="keywordtype">int</span> l,<span class="keywordtype">double</span> dx,<span class="keywordtype">double</span> dy,<span class="keywordtype">double</span> dz);
<a name="l00206"></a>00206                 <span class="keyword">inline</span> <span class="keywordtype">void</span> remap(<span class="keywordtype">int</span> &amp;ai,<span class="keywordtype">int</span> &amp;aj,<span class="keywordtype">int</span> &amp;ak,<span class="keywordtype">int</span> &amp;ci,<span class="keywordtype">int</span> &amp;cj,<span class="keywordtype">int</span> &amp;ck,<span class="keywordtype">double</span> &amp;x,<span class="keywordtype">double</span> &amp;y,<span class="keywordtype">double</span> &amp;z,<span class="keywordtype">int</span> &amp;ijk);
<a name="l00207"></a>00207 };
<a name="l00208"></a>00208 <span class="comment"></span>
<a name="l00209"></a>00209 <span class="comment">/** \brief Extension of the container_periodic_base class for computing regular</span>
<a name="l00210"></a>00210 <span class="comment"> * Voronoi tessellations.</span>
<a name="l00211"></a>00211 <span class="comment"> *</span>
<a name="l00212"></a>00212 <span class="comment"> * This class is an extension of the container_periodic_base that has routines</span>
<a name="l00213"></a>00213 <span class="comment"> * specifically for computing the regular Voronoi tessellation with no</span>
<a name="l00214"></a>00214 <span class="comment"> * dependence on particle radii. */</span>
<a name="l00215"></a><a class="code" href="classvoro_1_1container__periodic.html">00215</a> <span class="keyword">class </span><a class="code" href="classvoro_1_1container__periodic.html" title="Extension of the container_periodic_base class for computing regular Voronoi tessellations.">container_periodic</a> : <span class="keyword">public</span> <a class="code" href="classvoro_1_1container__periodic__base.html" title="Class for representing a particle system in a 3D periodic non-orthogonal periodic domain...">container_periodic_base</a>, <span class="keyword">public</span> <a class="code" href="classvoro_1_1radius__mono.html" title="Class containing all of the routines that are specific to computing the regular Voronoi tessellation...">radius_mono</a> {
<a name="l00216"></a>00216         <span class="keyword">public</span>:
<a name="l00217"></a>00217                 <a class="code" href="classvoro_1_1container__periodic.html" title="Extension of the container_periodic_base class for computing regular Voronoi tessellations.">container_periodic</a>(<span class="keywordtype">double</span> bx_,<span class="keywordtype">double</span> bxy_,<span class="keywordtype">double</span> by_,<span class="keywordtype">double</span> bxz_,<span class="keywordtype">double</span> byz_,<span class="keywordtype">double</span> bz_,
<a name="l00218"></a>00218                                 <span class="keywordtype">int</span> nx_,<span class="keywordtype">int</span> ny_,<span class="keywordtype">int</span> nz_,<span class="keywordtype">int</span> init_mem_);
<a name="l00219"></a>00219                 <span class="keywordtype">void</span> clear();
<a name="l00220"></a>00220                 <span class="keywordtype">void</span> put(<span class="keywordtype">int</span> n,<span class="keywordtype">double</span> x,<span class="keywordtype">double</span> y,<span class="keywordtype">double</span> z);
<a name="l00221"></a>00221                 <span class="keywordtype">void</span> put(<span class="keywordtype">int</span> n,<span class="keywordtype">double</span> x,<span class="keywordtype">double</span> y,<span class="keywordtype">double</span> z,<span class="keywordtype">int</span> &amp;ai,<span class="keywordtype">int</span> &amp;aj,<span class="keywordtype">int</span> &amp;ak);
<a name="l00222"></a>00222                 <span class="keywordtype">void</span> put(<a class="code" href="classvoro_1_1particle__order.html" title="A class for storing ordering information when particles are added to a container.">particle_order</a> &amp;vo,<span class="keywordtype">int</span> n,<span class="keywordtype">double</span> x,<span class="keywordtype">double</span> y,<span class="keywordtype">double</span> z);
<a name="l00223"></a>00223                 <span class="keywordtype">void</span> <span class="keyword">import</span>(FILE *fp=stdin);
<a name="l00224"></a>00224                 <span class="keywordtype">void</span> <span class="keyword">import</span>(<a class="code" href="classvoro_1_1particle__order.html" title="A class for storing ordering information when particles are added to a container.">particle_order</a> &amp;vo,FILE *fp=stdin);<span class="comment"></span>
<a name="l00225"></a>00225 <span class="comment">                /** Imports a list of particles from an open file stream into</span>
<a name="l00226"></a>00226 <span class="comment">                 * the container. Entries of four numbers (Particle ID, x</span>
<a name="l00227"></a>00227 <span class="comment">                 * position, y position, z position) are searched for. If the</span>
<a name="l00228"></a>00228 <span class="comment">                 * file cannot be successfully read, then the routine causes a</span>
<a name="l00229"></a>00229 <span class="comment">                 * fatal error.</span>
<a name="l00230"></a>00230 <span class="comment">                 * \param[in] filename the name of the file to open and read</span>
<a name="l00231"></a>00231 <span class="comment">                 *                     from. */</span>
<a name="l00232"></a><a class="code" href="classvoro_1_1container__periodic.html#ac2b38542ffabd95cb7f5bc5dab162a5d">00232</a>                 <span class="keyword">inline</span> <span class="keywordtype">void</span> <span class="keyword">import</span>(<span class="keyword">const</span> <span class="keywordtype">char</span>* filename) {
<a name="l00233"></a>00233                         FILE *fp=safe_fopen(filename,<span class="stringliteral">&quot;r&quot;</span>);
<a name="l00234"></a>00234                         <span class="keyword">import</span>(fp);
<a name="l00235"></a>00235                         fclose(fp);
<a name="l00236"></a>00236                 }<span class="comment"></span>
<a name="l00237"></a>00237 <span class="comment">                /** Imports a list of particles from an open file stream into</span>
<a name="l00238"></a>00238 <span class="comment">                 * the container. Entries of four numbers (Particle ID, x</span>
<a name="l00239"></a>00239 <span class="comment">                 * position, y position, z position) are searched for. In</span>
<a name="l00240"></a>00240 <span class="comment">                 * addition, the order in which particles are read is saved</span>
<a name="l00241"></a>00241 <span class="comment">                 * into an ordering class. If the file cannot be successfully</span>
<a name="l00242"></a>00242 <span class="comment">                 * read, then the routine causes a fatal error.</span>
<a name="l00243"></a>00243 <span class="comment">                 * \param[in,out] vo the ordering class to use.</span>
<a name="l00244"></a>00244 <span class="comment">                 * \param[in] filename the name of the file to open and read</span>
<a name="l00245"></a>00245 <span class="comment">                 *                     from. */</span>
<a name="l00246"></a><a class="code" href="classvoro_1_1container__periodic.html#ae586c7cf716fa84e91e9f801f5ac8a50">00246</a>                 <span class="keyword">inline</span> <span class="keywordtype">void</span> <span class="keyword">import</span>(<a class="code" href="classvoro_1_1particle__order.html" title="A class for storing ordering information when particles are added to a container.">particle_order</a> &amp;vo,<span class="keyword">const</span> <span class="keywordtype">char</span>* filename) {
<a name="l00247"></a>00247                         FILE *fp=safe_fopen(filename,<span class="stringliteral">&quot;r&quot;</span>);
<a name="l00248"></a>00248                         <span class="keyword">import</span>(vo,fp);
<a name="l00249"></a>00249                         fclose(fp);
<a name="l00250"></a>00250                 }
<a name="l00251"></a>00251                 <span class="keywordtype">void</span> compute_all_cells();
<a name="l00252"></a>00252                 <span class="keywordtype">double</span> sum_cell_volumes();<span class="comment"></span>
<a name="l00253"></a>00253 <span class="comment">                /** Dumps particle IDs and positions to a file.</span>
<a name="l00254"></a>00254 <span class="comment">                 * \param[in] vl the loop class to use.</span>
<a name="l00255"></a>00255 <span class="comment">                 * \param[in] fp a file handle to write to. */</span>
<a name="l00256"></a>00256                 <span class="keyword">template</span>&lt;<span class="keyword">class</span> c_loop&gt;
<a name="l00257"></a><a class="code" href="classvoro_1_1container__periodic.html#a4b22d1868b96f049891a4f65e57497e8">00257</a>                 <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic.html#a4b22d1868b96f049891a4f65e57497e8">draw_particles</a>(c_loop &amp;vl,FILE *fp) {
<a name="l00258"></a>00258                         <span class="keywordtype">double</span> *pp;
<a name="l00259"></a>00259                         <span class="keywordflow">if</span>(vl.start()) <span class="keywordflow">do</span> {
<a name="l00260"></a>00260                                 pp=p[vl.ijk]+3*vl.q;
<a name="l00261"></a>00261                                 fprintf(fp,<span class="stringliteral">&quot;%d %g %g %g\n&quot;</span>,<span class="keywordtype">id</span>[vl.ijk][vl.q],*pp,pp[1],pp[2]);
<a name="l00262"></a>00262                         } <span class="keywordflow">while</span>(vl.inc());
<a name="l00263"></a>00263                 }<span class="comment"></span>
<a name="l00264"></a>00264 <span class="comment">                /** Dumps all of the particle IDs and positions to a file.</span>
<a name="l00265"></a>00265 <span class="comment">                 * \param[in] fp a file handle to write to. */</span>
<a name="l00266"></a><a class="code" href="classvoro_1_1container__periodic.html#a21a12c0ed7e67de10360cd3af8a5928f">00266</a>                 <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic.html#a21a12c0ed7e67de10360cd3af8a5928f">draw_particles</a>(FILE *fp=stdout) {
<a name="l00267"></a>00267                         <a class="code" href="classvoro_1_1c__loop__all__periodic.html" title="A class for looping over all particles in a container_periodic or container_periodic_poly class...">c_loop_all_periodic</a> vl(*<span class="keyword">this</span>);
<a name="l00268"></a>00268                         draw_particles(vl,fp);
<a name="l00269"></a>00269                 }<span class="comment"></span>
<a name="l00270"></a>00270 <span class="comment">                /** Dumps all of the particle IDs and positions to a file.</span>
<a name="l00271"></a>00271 <span class="comment">                 * \param[in] filename the name of the file to write to. */</span>
<a name="l00272"></a><a class="code" href="classvoro_1_1container__periodic.html#a0b7b5b922f383d0c8d05e499a887a3b9">00272</a>                 <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic.html#a0b7b5b922f383d0c8d05e499a887a3b9">draw_particles</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *filename) {
<a name="l00273"></a>00273                         FILE *fp=safe_fopen(filename,<span class="stringliteral">&quot;w&quot;</span>);
<a name="l00274"></a>00274                         draw_particles(fp);
<a name="l00275"></a>00275                         fclose(fp);
<a name="l00276"></a>00276                 }<span class="comment"></span>
<a name="l00277"></a>00277 <span class="comment">                /** Dumps particle positions in POV-Ray format.</span>
<a name="l00278"></a>00278 <span class="comment">                 * \param[in] vl the loop class to use.</span>
<a name="l00279"></a>00279 <span class="comment">                 * \param[in] fp a file handle to write to. */</span>
<a name="l00280"></a>00280                 <span class="keyword">template</span>&lt;<span class="keyword">class</span> c_loop&gt;
<a name="l00281"></a><a class="code" href="classvoro_1_1container__periodic.html#a7086ad4c901827134b29a1bfc1b0bd3d">00281</a>                 <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic.html#a7086ad4c901827134b29a1bfc1b0bd3d">draw_particles_pov</a>(c_loop &amp;vl,FILE *fp) {
<a name="l00282"></a>00282                         <span class="keywordtype">double</span> *pp;
<a name="l00283"></a>00283                         <span class="keywordflow">if</span>(vl.start()) <span class="keywordflow">do</span> {
<a name="l00284"></a>00284                                 pp=p[vl.ijk]+3*vl.q;
<a name="l00285"></a>00285                                 fprintf(fp,<span class="stringliteral">&quot;// id %d\nsphere{&lt;%g,%g,%g&gt;,s}\n&quot;</span>,
<a name="l00286"></a>00286                                                 <span class="keywordtype">id</span>[vl.ijk][vl.q],*pp,pp[1],pp[2]);
<a name="l00287"></a>00287                         } <span class="keywordflow">while</span>(vl.inc());
<a name="l00288"></a>00288                 }<span class="comment"></span>
<a name="l00289"></a>00289 <span class="comment">                /** Dumps all particle positions in POV-Ray format.</span>
<a name="l00290"></a>00290 <span class="comment">                 * \param[in] fp a file handle to write to. */</span>
<a name="l00291"></a><a class="code" href="classvoro_1_1container__periodic.html#a7279993d74b79966cfaeab40f8df5882">00291</a>                 <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic.html#a7279993d74b79966cfaeab40f8df5882">draw_particles_pov</a>(FILE *fp=stdout) {
<a name="l00292"></a>00292                         <a class="code" href="classvoro_1_1c__loop__all__periodic.html" title="A class for looping over all particles in a container_periodic or container_periodic_poly class...">c_loop_all_periodic</a> vl(*<span class="keyword">this</span>);
<a name="l00293"></a>00293                         draw_particles_pov(vl,fp);
<a name="l00294"></a>00294                 }<span class="comment"></span>
<a name="l00295"></a>00295 <span class="comment">                /** Dumps all particle positions in POV-Ray format.</span>
<a name="l00296"></a>00296 <span class="comment">                 * \param[in] filename the name of the file to write to. */</span>
<a name="l00297"></a><a class="code" href="classvoro_1_1container__periodic.html#af008d47998b895aeeb108361a642407d">00297</a>                 <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic.html#af008d47998b895aeeb108361a642407d">draw_particles_pov</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *filename) {
<a name="l00298"></a>00298                         FILE *fp=safe_fopen(filename,<span class="stringliteral">&quot;w&quot;</span>);
<a name="l00299"></a>00299                         draw_particles_pov(fp);
<a name="l00300"></a>00300                         fclose(fp);
<a name="l00301"></a>00301                 }<span class="comment"></span>
<a name="l00302"></a>00302 <span class="comment">                /** Computes Voronoi cells and saves the output in gnuplot</span>
<a name="l00303"></a>00303 <span class="comment">                 * format.</span>
<a name="l00304"></a>00304 <span class="comment">                 * \param[in] vl the loop class to use.</span>
<a name="l00305"></a>00305 <span class="comment">                 * \param[in] fp a file handle to write to. */</span>
<a name="l00306"></a>00306                 <span class="keyword">template</span>&lt;<span class="keyword">class</span> c_loop&gt;
<a name="l00307"></a><a class="code" href="classvoro_1_1container__periodic.html#ad90cf825d916a83570382f7cfae0461b">00307</a>                 <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic.html#ad90cf825d916a83570382f7cfae0461b">draw_cells_gnuplot</a>(c_loop &amp;vl,FILE *fp) {
<a name="l00308"></a>00308                         <a class="code" href="classvoro_1_1voronoicell.html" title="Extension of the voronoicell_base class to represent a Voronoi cell without neighbor information...">voronoicell</a> c;<span class="keywordtype">double</span> *pp;
<a name="l00309"></a>00309                         <span class="keywordflow">if</span>(vl.start()) <span class="keywordflow">do</span> <span class="keywordflow">if</span>(compute_cell(c,vl)) {
<a name="l00310"></a>00310                                 pp=p[vl.ijk]+ps*vl.q;
<a name="l00311"></a>00311                                 c.<a class="code" href="classvoro_1_1voronoicell__base.html#a1c0657c1d89313089bbd437170c97d46">draw_gnuplot</a>(*pp,pp[1],pp[2],fp);
<a name="l00312"></a>00312                         } <span class="keywordflow">while</span>(vl.inc());
<a name="l00313"></a>00313                 }<span class="comment"></span>
<a name="l00314"></a>00314 <span class="comment">                /** Computes all Voronoi cells and saves the output in gnuplot</span>
<a name="l00315"></a>00315 <span class="comment">                 * format.</span>
<a name="l00316"></a>00316 <span class="comment">                 * \param[in] fp a file handle to write to. */</span>
<a name="l00317"></a><a class="code" href="classvoro_1_1container__periodic.html#adaf8256dd86c8c37618113cee774345f">00317</a>                 <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic.html#adaf8256dd86c8c37618113cee774345f">draw_cells_gnuplot</a>(FILE *fp=stdout) {
<a name="l00318"></a>00318                         <a class="code" href="classvoro_1_1c__loop__all__periodic.html" title="A class for looping over all particles in a container_periodic or container_periodic_poly class...">c_loop_all_periodic</a> vl(*<span class="keyword">this</span>);
<a name="l00319"></a>00319                         draw_cells_gnuplot(vl,fp);
<a name="l00320"></a>00320                 }<span class="comment"></span>
<a name="l00321"></a>00321 <span class="comment">                /** Compute all Voronoi cells and saves the output in gnuplot</span>
<a name="l00322"></a>00322 <span class="comment">                 * format.</span>
<a name="l00323"></a>00323 <span class="comment">                 * \param[in] filename the name of the file to write to. */</span>
<a name="l00324"></a><a class="code" href="classvoro_1_1container__periodic.html#a4f2b088d20b479b62a3dcdfa42d62526">00324</a>                 <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic.html#a4f2b088d20b479b62a3dcdfa42d62526">draw_cells_gnuplot</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *filename) {
<a name="l00325"></a>00325                         FILE *fp=safe_fopen(filename,<span class="stringliteral">&quot;w&quot;</span>);
<a name="l00326"></a>00326                         draw_cells_gnuplot(fp);
<a name="l00327"></a>00327                         fclose(fp);
<a name="l00328"></a>00328                 }<span class="comment"></span>
<a name="l00329"></a>00329 <span class="comment">                /** Computes Voronoi cells and saves the output in POV-Ray</span>
<a name="l00330"></a>00330 <span class="comment">                 * format.</span>
<a name="l00331"></a>00331 <span class="comment">                 * \param[in] vl the loop class to use.</span>
<a name="l00332"></a>00332 <span class="comment">                 * \param[in] fp a file handle to write to. */</span>
<a name="l00333"></a>00333                 <span class="keyword">template</span>&lt;<span class="keyword">class</span> c_loop&gt;
<a name="l00334"></a><a class="code" href="classvoro_1_1container__periodic.html#adba11c6b4f9a20b1d5e0e16b94fe7dff">00334</a>                 <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic.html#adba11c6b4f9a20b1d5e0e16b94fe7dff">draw_cells_pov</a>(c_loop &amp;vl,FILE *fp) {
<a name="l00335"></a>00335                         <a class="code" href="classvoro_1_1voronoicell.html" title="Extension of the voronoicell_base class to represent a Voronoi cell without neighbor information...">voronoicell</a> c;<span class="keywordtype">double</span> *pp;
<a name="l00336"></a>00336                         <span class="keywordflow">if</span>(vl.start()) <span class="keywordflow">do</span> <span class="keywordflow">if</span>(compute_cell(c,vl)) {
<a name="l00337"></a>00337                                 fprintf(fp,<span class="stringliteral">&quot;// cell %d\n&quot;</span>,<span class="keywordtype">id</span>[vl.ijk][vl.q]);
<a name="l00338"></a>00338                                 pp=p[vl.ijk]+ps*vl.q;
<a name="l00339"></a>00339                                 c.<a class="code" href="classvoro_1_1voronoicell__base.html#a923ffa62bd5d62070cd29e01f3a1327a">draw_pov</a>(*pp,pp[1],pp[2],fp);
<a name="l00340"></a>00340                         } <span class="keywordflow">while</span>(vl.inc());
<a name="l00341"></a>00341                 }<span class="comment"></span>
<a name="l00342"></a>00342 <span class="comment">                /** Computes all Voronoi cells and saves the output in POV-Ray</span>
<a name="l00343"></a>00343 <span class="comment">                 * format.</span>
<a name="l00344"></a>00344 <span class="comment">                 * \param[in] fp a file handle to write to. */</span>
<a name="l00345"></a><a class="code" href="classvoro_1_1container__periodic.html#ae35a7e24438d3290c5dbb39f2474f3f4">00345</a>                 <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic.html#ae35a7e24438d3290c5dbb39f2474f3f4">draw_cells_pov</a>(FILE *fp=stdout) {
<a name="l00346"></a>00346                         <a class="code" href="classvoro_1_1c__loop__all__periodic.html" title="A class for looping over all particles in a container_periodic or container_periodic_poly class...">c_loop_all_periodic</a> vl(*<span class="keyword">this</span>);
<a name="l00347"></a>00347                         draw_cells_pov(vl,fp);
<a name="l00348"></a>00348                 }<span class="comment"></span>
<a name="l00349"></a>00349 <span class="comment">                /** Computes all Voronoi cells and saves the output in POV-Ray</span>
<a name="l00350"></a>00350 <span class="comment">                 * format.</span>
<a name="l00351"></a>00351 <span class="comment">                 * \param[in] filename the name of the file to write to. */</span>
<a name="l00352"></a><a class="code" href="classvoro_1_1container__periodic.html#a690edc7e6e23393d82faf320aac1b2d9">00352</a>                 <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic.html#a690edc7e6e23393d82faf320aac1b2d9">draw_cells_pov</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *filename) {
<a name="l00353"></a>00353                         FILE *fp=safe_fopen(filename,<span class="stringliteral">&quot;w&quot;</span>);
<a name="l00354"></a>00354                         draw_cells_pov(fp);
<a name="l00355"></a>00355                         fclose(fp);
<a name="l00356"></a>00356                 }<span class="comment"></span>
<a name="l00357"></a>00357 <span class="comment">                /** Computes the Voronoi cells and saves customized information</span>
<a name="l00358"></a>00358 <span class="comment">                 * about them.</span>
<a name="l00359"></a>00359 <span class="comment">                 * \param[in] vl the loop class to use.</span>
<a name="l00360"></a>00360 <span class="comment">                 * \param[in] format the custom output string to use.</span>
<a name="l00361"></a>00361 <span class="comment">                 * \param[in] fp a file handle to write to. */</span>
<a name="l00362"></a>00362                 <span class="keyword">template</span>&lt;<span class="keyword">class</span> c_loop&gt;
<a name="l00363"></a><a class="code" href="classvoro_1_1container__periodic.html#adeb50c6841166e59a6be150d7adb4212">00363</a>                 <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic.html#adeb50c6841166e59a6be150d7adb4212">print_custom</a>(c_loop &amp;vl,<span class="keyword">const</span> <span class="keywordtype">char</span> *format,FILE *fp) {
<a name="l00364"></a>00364                         <span class="keywordtype">int</span> ijk,q;<span class="keywordtype">double</span> *pp;
<a name="l00365"></a>00365                         <span class="keywordflow">if</span>(contains_neighbor(format)) {
<a name="l00366"></a>00366                                 <a class="code" href="classvoro_1_1voronoicell__neighbor.html" title="Extension of the voronoicell_base class to represent a Voronoi cell with neighbor information...">voronoicell_neighbor</a> c;
<a name="l00367"></a>00367                                 <span class="keywordflow">if</span>(vl.start()) <span class="keywordflow">do</span> <span class="keywordflow">if</span>(compute_cell(c,vl)) {
<a name="l00368"></a>00368                                         ijk=vl.ijk;q=vl.q;pp=p[ijk]+ps*q;
<a name="l00369"></a>00369                                         c.<a class="code" href="classvoro_1_1voronoicell__base.html#a095c6bfc1b9b7a087d0b35b443e5c023">output_custom</a>(format,<span class="keywordtype">id</span>[ijk][q],*pp,pp[1],pp[2],default_radius,fp);
<a name="l00370"></a>00370                                 } <span class="keywordflow">while</span>(vl.inc());
<a name="l00371"></a>00371                         } <span class="keywordflow">else</span> {
<a name="l00372"></a>00372                                 <a class="code" href="classvoro_1_1voronoicell.html" title="Extension of the voronoicell_base class to represent a Voronoi cell without neighbor information...">voronoicell</a> c;
<a name="l00373"></a>00373                                 <span class="keywordflow">if</span>(vl.start()) <span class="keywordflow">do</span> <span class="keywordflow">if</span>(compute_cell(c,vl)) {
<a name="l00374"></a>00374                                         ijk=vl.ijk;q=vl.q;pp=p[ijk]+ps*q;
<a name="l00375"></a>00375                                         c.<a class="code" href="classvoro_1_1voronoicell__base.html#a095c6bfc1b9b7a087d0b35b443e5c023">output_custom</a>(format,<span class="keywordtype">id</span>[ijk][q],*pp,pp[1],pp[2],default_radius,fp);
<a name="l00376"></a>00376                                 } <span class="keywordflow">while</span>(vl.inc());
<a name="l00377"></a>00377                         }
<a name="l00378"></a>00378                 }
<a name="l00379"></a>00379                 <span class="keywordtype">void</span> print_custom(<span class="keyword">const</span> <span class="keywordtype">char</span> *format,FILE *fp=stdout);
<a name="l00380"></a>00380                 <span class="keywordtype">void</span> print_custom(<span class="keyword">const</span> <span class="keywordtype">char</span> *format,<span class="keyword">const</span> <span class="keywordtype">char</span> *filename);
<a name="l00381"></a>00381                 <span class="keywordtype">bool</span> find_voronoi_cell(<span class="keywordtype">double</span> x,<span class="keywordtype">double</span> y,<span class="keywordtype">double</span> z,<span class="keywordtype">double</span> &amp;rx,<span class="keywordtype">double</span> &amp;ry,<span class="keywordtype">double</span> &amp;rz,<span class="keywordtype">int</span> &amp;pid);<span class="comment"></span>
<a name="l00382"></a>00382 <span class="comment">                /** Computes the Voronoi cell for a particle currently being</span>
<a name="l00383"></a>00383 <span class="comment">                 * referenced by a loop class.</span>
<a name="l00384"></a>00384 <span class="comment">                 * \param[out] c a Voronoi cell class in which to store the</span>
<a name="l00385"></a>00385 <span class="comment">                 *               computed cell.</span>
<a name="l00386"></a>00386 <span class="comment">                 * \param[in] vl the loop class to use.</span>
<a name="l00387"></a>00387 <span class="comment">                 * \return True if the cell was computed. If the cell cannot be</span>
<a name="l00388"></a>00388 <span class="comment">                 * computed because it was removed entirely for some reason,</span>
<a name="l00389"></a>00389 <span class="comment">                 * then the routine returns false. */</span>
<a name="l00390"></a>00390                 <span class="keyword">template</span>&lt;<span class="keyword">class</span> v_cell,<span class="keyword">class</span> c_loop&gt;
<a name="l00391"></a><a class="code" href="classvoro_1_1container__periodic.html#af5cc004a3be4a1eecb037fe9f4b9e2ff">00391</a>                 <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="classvoro_1_1container__periodic.html#af5cc004a3be4a1eecb037fe9f4b9e2ff">compute_cell</a>(v_cell &amp;c,c_loop &amp;vl) {
<a name="l00392"></a>00392                         <span class="keywordflow">return</span> vc.compute_cell(c,vl.ijk,vl.q,vl.i,vl.j,vl.k);
<a name="l00393"></a>00393                 }<span class="comment"></span>
<a name="l00394"></a>00394 <span class="comment">                /** Computes the Voronoi cell for given particle.</span>
<a name="l00395"></a>00395 <span class="comment">                 * \param[out] c a Voronoi cell class in which to store the</span>
<a name="l00396"></a>00396 <span class="comment">                 *               computed cell.</span>
<a name="l00397"></a>00397 <span class="comment">                 * \param[in] ijk the block that the particle is within.</span>
<a name="l00398"></a>00398 <span class="comment">                 * \param[in] q the index of the particle within the block.</span>
<a name="l00399"></a>00399 <span class="comment">                 * \return True if the cell was computed. If the cell cannot be</span>
<a name="l00400"></a>00400 <span class="comment">                 * computed because it was removed entirely for some reason,</span>
<a name="l00401"></a>00401 <span class="comment">                 * then the routine returns false. */</span>
<a name="l00402"></a>00402                 <span class="keyword">template</span>&lt;<span class="keyword">class</span> v_cell&gt;
<a name="l00403"></a><a class="code" href="classvoro_1_1container__periodic.html#a5ed9e19316148b6af242887ccc8ccf60">00403</a>                 <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="classvoro_1_1container__periodic.html#a5ed9e19316148b6af242887ccc8ccf60">compute_cell</a>(v_cell &amp;c,<span class="keywordtype">int</span> ijk,<span class="keywordtype">int</span> q) {
<a name="l00404"></a>00404                         <span class="keywordtype">int</span> k(ijk/(nx*oy)),ijkt(ijk-(nx*oy)*k),j(ijkt/nx),i(ijkt-j*nx);
<a name="l00405"></a>00405                         <span class="keywordflow">return</span> vc.compute_cell(c,ijk,q,i,j,k);
<a name="l00406"></a>00406                 }
<a name="l00407"></a>00407         <span class="keyword">private</span>:
<a name="l00408"></a>00408                 <a class="code" href="classvoro_1_1voro__compute.html">voro_compute&lt;container_periodic&gt;</a> vc;
<a name="l00409"></a>00409                 <span class="keyword">friend</span> <span class="keyword">class </span><a class="code" href="classvoro_1_1voro__compute.html" title="Template for carrying out Voronoi cell computations.">voro_compute</a>&lt;<a class="code" href="classvoro_1_1container__periodic.html" title="Extension of the container_periodic_base class for computing regular Voronoi tessellations.">container_periodic</a>&gt;;
<a name="l00410"></a>00410 };
<a name="l00411"></a>00411 <span class="comment"></span>
<a name="l00412"></a>00412 <span class="comment">/** \brief Extension of the container_periodic_base class for computing radical</span>
<a name="l00413"></a>00413 <span class="comment"> * Voronoi tessellations.</span>
<a name="l00414"></a>00414 <span class="comment"> *</span>
<a name="l00415"></a>00415 <span class="comment"> * This class is an extension of container_periodic_base that has routines</span>
<a name="l00416"></a>00416 <span class="comment"> * specifically for computing the radical Voronoi tessellation that depends</span>
<a name="l00417"></a>00417 <span class="comment"> * on the particle radii. */</span>
<a name="l00418"></a><a class="code" href="classvoro_1_1container__periodic__poly.html">00418</a> <span class="keyword">class </span><a class="code" href="classvoro_1_1container__periodic__poly.html" title="Extension of the container_periodic_base class for computing radical Voronoi tessellations.">container_periodic_poly</a> : <span class="keyword">public</span> <a class="code" href="classvoro_1_1container__periodic__base.html" title="Class for representing a particle system in a 3D periodic non-orthogonal periodic domain...">container_periodic_base</a>, <span class="keyword">public</span> <a class="code" href="classvoro_1_1radius__poly.html" title="Class containing all of the routines that are specific to computing the radical Voronoi tessellation...">radius_poly</a> {
<a name="l00419"></a>00419         <span class="keyword">public</span>:
<a name="l00420"></a>00420                 <a class="code" href="classvoro_1_1container__periodic__poly.html" title="Extension of the container_periodic_base class for computing radical Voronoi tessellations.">container_periodic_poly</a>(<span class="keywordtype">double</span> bx_,<span class="keywordtype">double</span> bxy_,<span class="keywordtype">double</span> by_,<span class="keywordtype">double</span> bxz_,<span class="keywordtype">double</span> byz_,<span class="keywordtype">double</span> bz_,
<a name="l00421"></a>00421                                 <span class="keywordtype">int</span> nx_,<span class="keywordtype">int</span> ny_,<span class="keywordtype">int</span> nz_,<span class="keywordtype">int</span> init_mem_);
<a name="l00422"></a>00422                 <span class="keywordtype">void</span> clear();
<a name="l00423"></a>00423                 <span class="keywordtype">void</span> put(<span class="keywordtype">int</span> n,<span class="keywordtype">double</span> x,<span class="keywordtype">double</span> y,<span class="keywordtype">double</span> z,<span class="keywordtype">double</span> r);
<a name="l00424"></a>00424                 <span class="keywordtype">void</span> put(<span class="keywordtype">int</span> n,<span class="keywordtype">double</span> x,<span class="keywordtype">double</span> y,<span class="keywordtype">double</span> z,<span class="keywordtype">double</span> r,<span class="keywordtype">int</span> &amp;ai,<span class="keywordtype">int</span> &amp;aj,<span class="keywordtype">int</span> &amp;ak);
<a name="l00425"></a>00425                 <span class="keywordtype">void</span> put(<a class="code" href="classvoro_1_1particle__order.html" title="A class for storing ordering information when particles are added to a container.">particle_order</a> &amp;vo,<span class="keywordtype">int</span> n,<span class="keywordtype">double</span> x,<span class="keywordtype">double</span> y,<span class="keywordtype">double</span> z,<span class="keywordtype">double</span> r);
<a name="l00426"></a>00426                 <span class="keywordtype">void</span> <span class="keyword">import</span>(FILE *fp=stdin);
<a name="l00427"></a>00427                 <span class="keywordtype">void</span> <span class="keyword">import</span>(<a class="code" href="classvoro_1_1particle__order.html" title="A class for storing ordering information when particles are added to a container.">particle_order</a> &amp;vo,FILE *fp=stdin);<span class="comment"></span>
<a name="l00428"></a>00428 <span class="comment">                /** Imports a list of particles from an open file stream into</span>
<a name="l00429"></a>00429 <span class="comment">                 * the container_poly class. Entries of five numbers (Particle</span>
<a name="l00430"></a>00430 <span class="comment">                 * ID, x position, y position, z position, radius) are searched</span>
<a name="l00431"></a>00431 <span class="comment">                 * for. If the file cannot be successfully read, then the</span>
<a name="l00432"></a>00432 <span class="comment">                 * routine causes a fatal error.</span>
<a name="l00433"></a>00433 <span class="comment">                 * \param[in] filename the name of the file to open and read</span>
<a name="l00434"></a>00434 <span class="comment">                 *                     from. */</span>
<a name="l00435"></a><a class="code" href="classvoro_1_1container__periodic__poly.html#a2052ab1ed4c33c961fbc26a86c66a494">00435</a>                 <span class="keyword">inline</span> <span class="keywordtype">void</span> <span class="keyword">import</span>(<span class="keyword">const</span> <span class="keywordtype">char</span>* filename) {
<a name="l00436"></a>00436                         FILE *fp=safe_fopen(filename,<span class="stringliteral">&quot;r&quot;</span>);
<a name="l00437"></a>00437                         <span class="keyword">import</span>(fp);
<a name="l00438"></a>00438                         fclose(fp);
<a name="l00439"></a>00439                 }<span class="comment"></span>
<a name="l00440"></a>00440 <span class="comment">                /** Imports a list of particles from an open file stream into</span>
<a name="l00441"></a>00441 <span class="comment">                 * the container_poly class. Entries of five numbers (Particle</span>
<a name="l00442"></a>00442 <span class="comment">                 * ID, x position, y position, z position, radius) are searched</span>
<a name="l00443"></a>00443 <span class="comment">                 * for. In addition, the order in which particles are read is</span>
<a name="l00444"></a>00444 <span class="comment">                 * saved into an ordering class. If the file cannot be</span>
<a name="l00445"></a>00445 <span class="comment">                 * successfully read, then the routine causes a fatal error.</span>
<a name="l00446"></a>00446 <span class="comment">                 * \param[in,out] vo the ordering class to use.</span>
<a name="l00447"></a>00447 <span class="comment">                 * \param[in] filename the name of the file to open and read</span>
<a name="l00448"></a>00448 <span class="comment">                 *                     from. */</span>
<a name="l00449"></a><a class="code" href="classvoro_1_1container__periodic__poly.html#a346b67c09850a78e8eb9144029fe3087">00449</a>                 <span class="keyword">inline</span> <span class="keywordtype">void</span> <span class="keyword">import</span>(<a class="code" href="classvoro_1_1particle__order.html" title="A class for storing ordering information when particles are added to a container.">particle_order</a> &amp;vo,<span class="keyword">const</span> <span class="keywordtype">char</span>* filename) {
<a name="l00450"></a>00450                         FILE *fp=safe_fopen(filename,<span class="stringliteral">&quot;r&quot;</span>);
<a name="l00451"></a>00451                         <span class="keyword">import</span>(vo,fp);
<a name="l00452"></a>00452                         fclose(fp);
<a name="l00453"></a>00453                 }
<a name="l00454"></a>00454                 <span class="keywordtype">void</span> compute_all_cells();
<a name="l00455"></a>00455                 <span class="keywordtype">double</span> sum_cell_volumes();<span class="comment"></span>
<a name="l00456"></a>00456 <span class="comment">                /** Dumps particle IDs, positions and radii to a file.</span>
<a name="l00457"></a>00457 <span class="comment">                 * \param[in] vl the loop class to use.</span>
<a name="l00458"></a>00458 <span class="comment">                 * \param[in] fp a file handle to write to. */</span>
<a name="l00459"></a>00459                 <span class="keyword">template</span>&lt;<span class="keyword">class</span> c_loop&gt;
<a name="l00460"></a><a class="code" href="classvoro_1_1container__periodic__poly.html#a3760b525f8c9dd5b360e6e4a80294d9a">00460</a>                 <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic__poly.html#a3760b525f8c9dd5b360e6e4a80294d9a">draw_particles</a>(c_loop &amp;vl,FILE *fp) {
<a name="l00461"></a>00461                         <span class="keywordtype">double</span> *pp;
<a name="l00462"></a>00462                         <span class="keywordflow">if</span>(vl.start()) <span class="keywordflow">do</span> {
<a name="l00463"></a>00463                                 pp=p[vl.ijk]+4*vl.q;
<a name="l00464"></a>00464                                 fprintf(fp,<span class="stringliteral">&quot;%d %g %g %g %g\n&quot;</span>,<span class="keywordtype">id</span>[vl.ijk][vl.q],*pp,pp[1],pp[2],pp[3]);
<a name="l00465"></a>00465                         } <span class="keywordflow">while</span>(vl.inc());
<a name="l00466"></a>00466                 }<span class="comment"></span>
<a name="l00467"></a>00467 <span class="comment">                /** Dumps all of the particle IDs, positions and radii to a</span>
<a name="l00468"></a>00468 <span class="comment">                 * file.</span>
<a name="l00469"></a>00469 <span class="comment">                 * \param[in] fp a file handle to write to. */</span>
<a name="l00470"></a><a class="code" href="classvoro_1_1container__periodic__poly.html#afa2993c7ef337244c73b073a3f546df7">00470</a>                 <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic__poly.html#afa2993c7ef337244c73b073a3f546df7">draw_particles</a>(FILE *fp=stdout) {
<a name="l00471"></a>00471                         <a class="code" href="classvoro_1_1c__loop__all__periodic.html" title="A class for looping over all particles in a container_periodic or container_periodic_poly class...">c_loop_all_periodic</a> vl(*<span class="keyword">this</span>);
<a name="l00472"></a>00472                         draw_particles(vl,fp);
<a name="l00473"></a>00473                 }<span class="comment"></span>
<a name="l00474"></a>00474 <span class="comment">                /** Dumps all of the particle IDs, positions and radii to a</span>
<a name="l00475"></a>00475 <span class="comment">                 * file.</span>
<a name="l00476"></a>00476 <span class="comment">                 * \param[in] filename the name of the file to write to. */</span>
<a name="l00477"></a><a class="code" href="classvoro_1_1container__periodic__poly.html#a7bfb4757df738760c59d4f8905a92c17">00477</a>                 <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic__poly.html#a7bfb4757df738760c59d4f8905a92c17">draw_particles</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *filename) {
<a name="l00478"></a>00478                         FILE *fp=safe_fopen(filename,<span class="stringliteral">&quot;w&quot;</span>);
<a name="l00479"></a>00479                         draw_particles(fp);
<a name="l00480"></a>00480                         fclose(fp);
<a name="l00481"></a>00481                 }<span class="comment"></span>
<a name="l00482"></a>00482 <span class="comment">                /** Dumps particle positions in POV-Ray format.</span>
<a name="l00483"></a>00483 <span class="comment">                 * \param[in] vl the loop class to use.</span>
<a name="l00484"></a>00484 <span class="comment">                 * \param[in] fp a file handle to write to. */</span>
<a name="l00485"></a>00485                 <span class="keyword">template</span>&lt;<span class="keyword">class</span> c_loop&gt;
<a name="l00486"></a><a class="code" href="classvoro_1_1container__periodic__poly.html#aa9c1c012d0826c2fd28682ded2dd90f1">00486</a>                 <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic__poly.html#aa9c1c012d0826c2fd28682ded2dd90f1">draw_particles_pov</a>(c_loop &amp;vl,FILE *fp) {
<a name="l00487"></a>00487                         <span class="keywordtype">double</span> *pp;
<a name="l00488"></a>00488                         <span class="keywordflow">if</span>(vl.start()) <span class="keywordflow">do</span> {
<a name="l00489"></a>00489                                 pp=p[vl.ijk]+4*vl.q;
<a name="l00490"></a>00490                                 fprintf(fp,<span class="stringliteral">&quot;// id %d\nsphere{&lt;%g,%g,%g&gt;,%g}\n&quot;</span>,
<a name="l00491"></a>00491                                                 <span class="keywordtype">id</span>[vl.ijk][vl.q],*pp,pp[1],pp[2],pp[3]);
<a name="l00492"></a>00492                         } <span class="keywordflow">while</span>(vl.inc());
<a name="l00493"></a>00493                 }<span class="comment"></span>
<a name="l00494"></a>00494 <span class="comment">                /** Dumps all the particle positions in POV-Ray format.</span>
<a name="l00495"></a>00495 <span class="comment">                 * \param[in] fp a file handle to write to. */</span>
<a name="l00496"></a><a class="code" href="classvoro_1_1container__periodic__poly.html#a5bf55c7e6ace75b00aa245636afb82b7">00496</a>                 <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic__poly.html#a5bf55c7e6ace75b00aa245636afb82b7">draw_particles_pov</a>(FILE *fp=stdout) {
<a name="l00497"></a>00497                         <a class="code" href="classvoro_1_1c__loop__all__periodic.html" title="A class for looping over all particles in a container_periodic or container_periodic_poly class...">c_loop_all_periodic</a> vl(*<span class="keyword">this</span>);
<a name="l00498"></a>00498                         draw_particles_pov(vl,fp);
<a name="l00499"></a>00499                 }<span class="comment"></span>
<a name="l00500"></a>00500 <span class="comment">                /** Dumps all the particle positions in POV-Ray format.</span>
<a name="l00501"></a>00501 <span class="comment">                 * \param[in] filename the name of the file to write to. */</span>
<a name="l00502"></a><a class="code" href="classvoro_1_1container__periodic__poly.html#acd3e09b90187ab0ebb521d16d914b9a0">00502</a>                 <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic__poly.html#acd3e09b90187ab0ebb521d16d914b9a0">draw_particles_pov</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *filename) {
<a name="l00503"></a>00503                         FILE *fp(safe_fopen(filename,<span class="stringliteral">&quot;w&quot;</span>));
<a name="l00504"></a>00504                         draw_particles_pov(fp);
<a name="l00505"></a>00505                         fclose(fp);
<a name="l00506"></a>00506                 }<span class="comment"></span>
<a name="l00507"></a>00507 <span class="comment">                /** Computes Voronoi cells and saves the output in gnuplot</span>
<a name="l00508"></a>00508 <span class="comment">                 * format.</span>
<a name="l00509"></a>00509 <span class="comment">                 * \param[in] vl the loop class to use.</span>
<a name="l00510"></a>00510 <span class="comment">                 * \param[in] fp a file handle to write to. */</span>
<a name="l00511"></a>00511                 <span class="keyword">template</span>&lt;<span class="keyword">class</span> c_loop&gt;
<a name="l00512"></a><a class="code" href="classvoro_1_1container__periodic__poly.html#aa4561672ab91f1064748dd18d340335c">00512</a>                 <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic__poly.html#aa4561672ab91f1064748dd18d340335c">draw_cells_gnuplot</a>(c_loop &amp;vl,FILE *fp) {
<a name="l00513"></a>00513                         <a class="code" href="classvoro_1_1voronoicell.html" title="Extension of the voronoicell_base class to represent a Voronoi cell without neighbor information...">voronoicell</a> c;<span class="keywordtype">double</span> *pp;
<a name="l00514"></a>00514                         <span class="keywordflow">if</span>(vl.start()) <span class="keywordflow">do</span> <span class="keywordflow">if</span>(compute_cell(c,vl)) {
<a name="l00515"></a>00515                                 pp=p[vl.ijk]+ps*vl.q;
<a name="l00516"></a>00516                                 c.<a class="code" href="classvoro_1_1voronoicell__base.html#a1c0657c1d89313089bbd437170c97d46">draw_gnuplot</a>(*pp,pp[1],pp[2],fp);
<a name="l00517"></a>00517                         } <span class="keywordflow">while</span>(vl.inc());
<a name="l00518"></a>00518                 }<span class="comment"></span>
<a name="l00519"></a>00519 <span class="comment">                /** Compute all Voronoi cells and saves the output in gnuplot</span>
<a name="l00520"></a>00520 <span class="comment">                 * format.</span>
<a name="l00521"></a>00521 <span class="comment">                 * \param[in] fp a file handle to write to. */</span>
<a name="l00522"></a><a class="code" href="classvoro_1_1container__periodic__poly.html#aed830c459b6f9b1a8ef130d0641c3ead">00522</a>                 <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic__poly.html#aed830c459b6f9b1a8ef130d0641c3ead">draw_cells_gnuplot</a>(FILE *fp=stdout) {
<a name="l00523"></a>00523                         <a class="code" href="classvoro_1_1c__loop__all__periodic.html" title="A class for looping over all particles in a container_periodic or container_periodic_poly class...">c_loop_all_periodic</a> vl(*<span class="keyword">this</span>);
<a name="l00524"></a>00524                         draw_cells_gnuplot(vl,fp);
<a name="l00525"></a>00525                 }<span class="comment"></span>
<a name="l00526"></a>00526 <span class="comment">                /** Compute all Voronoi cells and saves the output in gnuplot</span>
<a name="l00527"></a>00527 <span class="comment">                 * format.</span>
<a name="l00528"></a>00528 <span class="comment">                 * \param[in] filename the name of the file to write to. */</span>
<a name="l00529"></a><a class="code" href="classvoro_1_1container__periodic__poly.html#a6bfd38989da6891d35111ad61a5b3634">00529</a>                 <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic__poly.html#a6bfd38989da6891d35111ad61a5b3634">draw_cells_gnuplot</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *filename) {
<a name="l00530"></a>00530                         FILE *fp(safe_fopen(filename,<span class="stringliteral">&quot;w&quot;</span>));
<a name="l00531"></a>00531                         draw_cells_gnuplot(fp);
<a name="l00532"></a>00532                         fclose(fp);
<a name="l00533"></a>00533                 }<span class="comment"></span>
<a name="l00534"></a>00534 <span class="comment">                /** Computes Voronoi cells and saves the output in POV-Ray</span>
<a name="l00535"></a>00535 <span class="comment">                 * format.</span>
<a name="l00536"></a>00536 <span class="comment">                 * \param[in] vl the loop class to use.</span>
<a name="l00537"></a>00537 <span class="comment">                 * \param[in] fp a file handle to write to. */</span>
<a name="l00538"></a>00538                 <span class="keyword">template</span>&lt;<span class="keyword">class</span> c_loop&gt;
<a name="l00539"></a><a class="code" href="classvoro_1_1container__periodic__poly.html#a78c92412a5127918249bc9fbe14e6b52">00539</a>                 <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic__poly.html#a78c92412a5127918249bc9fbe14e6b52">draw_cells_pov</a>(c_loop &amp;vl,FILE *fp) {
<a name="l00540"></a>00540                         <a class="code" href="classvoro_1_1voronoicell.html" title="Extension of the voronoicell_base class to represent a Voronoi cell without neighbor information...">voronoicell</a> c;<span class="keywordtype">double</span> *pp;
<a name="l00541"></a>00541                         <span class="keywordflow">if</span>(vl.start()) <span class="keywordflow">do</span> <span class="keywordflow">if</span>(compute_cell(c,vl)) {
<a name="l00542"></a>00542                                 fprintf(fp,<span class="stringliteral">&quot;// cell %d\n&quot;</span>,<span class="keywordtype">id</span>[vl.ijk][vl.q]);
<a name="l00543"></a>00543                                 pp=p[vl.ijk]+ps*vl.q;
<a name="l00544"></a>00544                                 c.<a class="code" href="classvoro_1_1voronoicell__base.html#a923ffa62bd5d62070cd29e01f3a1327a">draw_pov</a>(*pp,pp[1],pp[2],fp);
<a name="l00545"></a>00545                         } <span class="keywordflow">while</span>(vl.inc());
<a name="l00546"></a>00546                 }<span class="comment"></span>
<a name="l00547"></a>00547 <span class="comment">                /** Computes all Voronoi cells and saves the output in POV-Ray</span>
<a name="l00548"></a>00548 <span class="comment">                 * format.</span>
<a name="l00549"></a>00549 <span class="comment">                 * \param[in] fp a file handle to write to. */</span>
<a name="l00550"></a><a class="code" href="classvoro_1_1container__periodic__poly.html#a23b1f79f3cc8cee7c4b4d9470a0ee6f0">00550</a>                 <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic__poly.html#a23b1f79f3cc8cee7c4b4d9470a0ee6f0">draw_cells_pov</a>(FILE *fp=stdout) {
<a name="l00551"></a>00551                         <a class="code" href="classvoro_1_1c__loop__all__periodic.html" title="A class for looping over all particles in a container_periodic or container_periodic_poly class...">c_loop_all_periodic</a> vl(*<span class="keyword">this</span>);
<a name="l00552"></a>00552                         draw_cells_pov(vl,fp);
<a name="l00553"></a>00553                 }<span class="comment"></span>
<a name="l00554"></a>00554 <span class="comment">                /** Computes all Voronoi cells and saves the output in POV-Ray</span>
<a name="l00555"></a>00555 <span class="comment">                 * format.</span>
<a name="l00556"></a>00556 <span class="comment">                 * \param[in] filename the name of the file to write to. */</span>
<a name="l00557"></a><a class="code" href="classvoro_1_1container__periodic__poly.html#a7f64711de2a4ce09c1cc2c0e5cbdf9f5">00557</a>                 <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic__poly.html#a7f64711de2a4ce09c1cc2c0e5cbdf9f5">draw_cells_pov</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *filename) {
<a name="l00558"></a>00558                         FILE *fp(safe_fopen(filename,<span class="stringliteral">&quot;w&quot;</span>));
<a name="l00559"></a>00559                         draw_cells_pov(fp);
<a name="l00560"></a>00560                         fclose(fp);
<a name="l00561"></a>00561                 }<span class="comment"></span>
<a name="l00562"></a>00562 <span class="comment">                /** Computes the Voronoi cells and saves customized information</span>
<a name="l00563"></a>00563 <span class="comment">                 * about them.</span>
<a name="l00564"></a>00564 <span class="comment">                 * \param[in] vl the loop class to use.</span>
<a name="l00565"></a>00565 <span class="comment">                 * \param[in] format the custom output string to use.</span>
<a name="l00566"></a>00566 <span class="comment">                 * \param[in] fp a file handle to write to. */</span>
<a name="l00567"></a>00567                 <span class="keyword">template</span>&lt;<span class="keyword">class</span> c_loop&gt;
<a name="l00568"></a><a class="code" href="classvoro_1_1container__periodic__poly.html#a7f4fc079c9386a4440417a38866acfa5">00568</a>                 <span class="keywordtype">void</span> <a class="code" href="classvoro_1_1container__periodic__poly.html#a7f4fc079c9386a4440417a38866acfa5">print_custom</a>(c_loop &amp;vl,<span class="keyword">const</span> <span class="keywordtype">char</span> *format,FILE *fp) {
<a name="l00569"></a>00569                         <span class="keywordtype">int</span> ijk,q;<span class="keywordtype">double</span> *pp;
<a name="l00570"></a>00570                         <span class="keywordflow">if</span>(contains_neighbor(format)) {
<a name="l00571"></a>00571                                 <a class="code" href="classvoro_1_1voronoicell__neighbor.html" title="Extension of the voronoicell_base class to represent a Voronoi cell with neighbor information...">voronoicell_neighbor</a> c;
<a name="l00572"></a>00572                                 <span class="keywordflow">if</span>(vl.start()) <span class="keywordflow">do</span> <span class="keywordflow">if</span>(compute_cell(c,vl)) {
<a name="l00573"></a>00573                                         ijk=vl.ijk;q=vl.q;pp=p[ijk]+ps*q;
<a name="l00574"></a>00574                                         c.<a class="code" href="classvoro_1_1voronoicell__base.html#a095c6bfc1b9b7a087d0b35b443e5c023">output_custom</a>(format,<span class="keywordtype">id</span>[ijk][q],*pp,pp[1],pp[2],pp[3],fp);
<a name="l00575"></a>00575                                 } <span class="keywordflow">while</span>(vl.inc());
<a name="l00576"></a>00576                         } <span class="keywordflow">else</span> {
<a name="l00577"></a>00577                                 <a class="code" href="classvoro_1_1voronoicell.html" title="Extension of the voronoicell_base class to represent a Voronoi cell without neighbor information...">voronoicell</a> c;
<a name="l00578"></a>00578                                 <span class="keywordflow">if</span>(vl.start()) <span class="keywordflow">do</span> <span class="keywordflow">if</span>(compute_cell(c,vl)) {
<a name="l00579"></a>00579                                         ijk=vl.ijk;q=vl.q;pp=p[ijk]+ps*q;
<a name="l00580"></a>00580                                         c.<a class="code" href="classvoro_1_1voronoicell__base.html#a095c6bfc1b9b7a087d0b35b443e5c023">output_custom</a>(format,<span class="keywordtype">id</span>[ijk][q],*pp,pp[1],pp[2],pp[3],fp);
<a name="l00581"></a>00581                                 } <span class="keywordflow">while</span>(vl.inc());
<a name="l00582"></a>00582                         }
<a name="l00583"></a>00583                 }<span class="comment"></span>
<a name="l00584"></a>00584 <span class="comment">                /** Computes the Voronoi cell for a particle currently being</span>
<a name="l00585"></a>00585 <span class="comment">                 * referenced by a loop class.</span>
<a name="l00586"></a>00586 <span class="comment">                 * \param[out] c a Voronoi cell class in which to store the</span>
<a name="l00587"></a>00587 <span class="comment">                 *               computed cell.</span>
<a name="l00588"></a>00588 <span class="comment">                 * \param[in] vl the loop class to use.</span>
<a name="l00589"></a>00589 <span class="comment">                 * \return True if the cell was computed. If the cell cannot be</span>
<a name="l00590"></a>00590 <span class="comment">                 * computed because it was removed entirely for some reason,</span>
<a name="l00591"></a>00591 <span class="comment">                 * then the routine returns false. */</span>
<a name="l00592"></a>00592                 <span class="keyword">template</span>&lt;<span class="keyword">class</span> v_cell,<span class="keyword">class</span> c_loop&gt;
<a name="l00593"></a><a class="code" href="classvoro_1_1container__periodic__poly.html#a399d6b409b62005a0da290a89c4fdadb">00593</a>                 <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="classvoro_1_1container__periodic__poly.html#a399d6b409b62005a0da290a89c4fdadb">compute_cell</a>(v_cell &amp;c,c_loop &amp;vl) {
<a name="l00594"></a>00594                         <span class="keywordflow">return</span> vc.compute_cell(c,vl.ijk,vl.q,vl.i,vl.j,vl.k);
<a name="l00595"></a>00595                 }<span class="comment"></span>
<a name="l00596"></a>00596 <span class="comment">                /** Computes the Voronoi cell for given particle.</span>
<a name="l00597"></a>00597 <span class="comment">                 * \param[out] c a Voronoi cell class in which to store the</span>
<a name="l00598"></a>00598 <span class="comment">                 *               computed cell.</span>
<a name="l00599"></a>00599 <span class="comment">                 * \param[in] ijk the block that the particle is within.</span>
<a name="l00600"></a>00600 <span class="comment">                 * \param[in] q the index of the particle within the block.</span>
<a name="l00601"></a>00601 <span class="comment">                 * \return True if the cell was computed. If the cell cannot be</span>
<a name="l00602"></a>00602 <span class="comment">                 * computed because it was removed entirely for some reason,</span>
<a name="l00603"></a>00603 <span class="comment">                 * then the routine returns false. */</span>
<a name="l00604"></a>00604                 <span class="keyword">template</span>&lt;<span class="keyword">class</span> v_cell&gt;
<a name="l00605"></a><a class="code" href="classvoro_1_1container__periodic__poly.html#abd0fd5314a1d1e50721d2320171064e8">00605</a>                 <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="classvoro_1_1container__periodic__poly.html#abd0fd5314a1d1e50721d2320171064e8">compute_cell</a>(v_cell &amp;c,<span class="keywordtype">int</span> ijk,<span class="keywordtype">int</span> q) {
<a name="l00606"></a>00606                         <span class="keywordtype">int</span> k(ijk/(nx*oy)),ijkt(ijk-(nx*oy)*k),j(ijkt/nx),i(ijkt-j*nx);
<a name="l00607"></a>00607                         <span class="keywordflow">return</span> vc.compute_cell(c,ijk,q,i,j,k);
<a name="l00608"></a>00608                 }
<a name="l00609"></a>00609                 <span class="keywordtype">void</span> print_custom(<span class="keyword">const</span> <span class="keywordtype">char</span> *format,FILE *fp=stdout);
<a name="l00610"></a>00610                 <span class="keywordtype">void</span> print_custom(<span class="keyword">const</span> <span class="keywordtype">char</span> *format,<span class="keyword">const</span> <span class="keywordtype">char</span> *filename);
<a name="l00611"></a>00611                 <span class="keywordtype">bool</span> find_voronoi_cell(<span class="keywordtype">double</span> x,<span class="keywordtype">double</span> y,<span class="keywordtype">double</span> z,<span class="keywordtype">double</span> &amp;rx,<span class="keywordtype">double</span> &amp;ry,<span class="keywordtype">double</span> &amp;rz,<span class="keywordtype">int</span> &amp;pid);
<a name="l00612"></a>00612         <span class="keyword">private</span>:
<a name="l00613"></a>00613                 <a class="code" href="classvoro_1_1voro__compute.html">voro_compute&lt;container_periodic_poly&gt;</a> vc;
<a name="l00614"></a>00614                 <span class="keyword">friend</span> <span class="keyword">class </span><a class="code" href="classvoro_1_1voro__compute.html" title="Template for carrying out Voronoi cell computations.">voro_compute</a>&lt;<a class="code" href="classvoro_1_1container__periodic__poly.html" title="Extension of the container_periodic_base class for computing radical Voronoi tessellations.">container_periodic_poly</a>&gt;;
<a name="l00615"></a>00615 };
<a name="l00616"></a>00616 
<a name="l00617"></a>00617 }
<a name="l00618"></a>00618 
<a name="l00619"></a>00619 <span class="preprocessor">#endif</span>
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